The Proteomics Shared Resource provides state-of-the-art protein technologies for cancer research with a focus on application of mass spectrometry and analytical chemistry. Services include: protein identification from samples in solution or in 1D or 2D gels; 2D gel electrophoresis, 2D-DIGE, image analysis, spot picking, and spot digestion; mass spectrometry analysis of protein complexes; membrane proteins; organellar proteomes and subproteomes; quantitative analysis of protein expression in different experimental conditions; posttranslational modifications; top-down analysis of proteins; development of biomarker and discovery projects; small molecule analysis by LC-MS, and hydrogen-deuterium exchange studies for protein dynamics. There is an adjacent computing area for offline mass spectrometry data analysis plus web-based searches and data mining. Major developments since the last review include a major renovation of the entire Proteomics facility and the installation of cooling equipment for temperature stabilization of instruments. Four new mass spectrometers (TOFTOF, LTQ linear trap, FT-ICR, QSTAR XL) were acquired along with a Typhoon fluorescence scanner. Several new highly qualified staff members have also been recruited. These include: Dr. Hui Xiao, an expert in FT-ICR mass spectrometry and hydrogen-deuterium exchange recruited from the University of Massachusetts, Amherst; Dr. Jihyeon Lim, also of Univ. of Mass., Amherst, an expert mass spectrometrist; and Dr. Fa-Yun Che, an expert in quantitative proteomics. Peptide synthesis was discontinued at the end of 2005 based upon the availability of high-quality peptides from companies in the commercial sector, allowing more effective utilization of personnel to support other critical services of high priority to users. The facility has played an important role in a variety of mass spectrometry applications that support high-priority AECC initiatives. These include development of transition-state enzyme inhibitors, the study of tubulin isoforms and microtubule-inhibitor binding sites, proteomic analyses as a predictor of breast cancer risk and for the prediction of response to treatment in squamous cell cancer of the head and neck. The facility has been active in the development of new methodologies to meet AECC investigator needs and in training AECC investigators so that they can use open-access laboratory equipment.